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Unverified Commit db5f55e5 authored by Nicolas Servant's avatar Nicolas Servant Committed by GitHub
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Merge pull request #65 from nservant/dev

Dev
parents 05dcc142 8ab27056
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...@@ -22,7 +22,7 @@ jobs: ...@@ -22,7 +22,7 @@ jobs:
- name: Pull docker image - name: Pull docker image
run: | run: |
docker pull nfcore/hic:dev docker pull nfcore/hic:dev
docker tag nfcore/hic:dev nfcore/hic:dev docker tag nfcore/hic:dev nfcore/hic:1.2.0
- name: Run pipeline with test data - name: Run pipeline with test data
run: | run: |
# nf-core: You can customise CI pipeline run tests as required # nf-core: You can customise CI pipeline run tests as required
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...@@ -3,11 +3,11 @@ ...@@ -3,11 +3,11 @@
The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html). and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
## v1.2.0dev - 2020-05-12 ## v1.2.0 - 2020-06-18
### `Added` ### `Added`
* Bump v1.2.0dev * Bump v1.2.0
* Merge template nf-core 1.9 * Merge template nf-core 1.9
* Move some options to camel_case * Move some options to camel_case
* Update python scripts for python3 * Update python scripts for python3
...@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0. ...@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
### `Fixed` ### `Fixed`
* Fix error in doc for Arima kit usage
* Sort output of `get_valid_interaction` process as the input files of `remove_duplicates` * Sort output of `get_valid_interaction` process as the input files of `remove_duplicates`
are expected to be sorted (sort -m) are expected to be sorted (sort -m)
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...@@ -7,8 +7,8 @@ RUN apt-get update && apt-get install -y gcc g++ && apt-get clean -y ...@@ -7,8 +7,8 @@ RUN apt-get update && apt-get install -y gcc g++ && apt-get clean -y
COPY environment.yml / COPY environment.yml /
RUN conda env create -f /environment.yml && conda clean -a RUN conda env create -f /environment.yml && conda clean -a
ENV PATH /opt/conda/envs/nf-core-hic-1.2.0dev/bin:$PATH ENV PATH /opt/conda/envs/nf-core-hic-1.2.0/bin:$PATH
# Dump the details of the installed packages to a file for posterity # Dump the details of the installed packages to a file for posterity
RUN conda env export --name nf-core-hic-1.2.0dev > nf-core-hic-1.2.0dev.yml RUN conda env export --name nf-core-hic-1.2.0 > nf-core-hic-1.2.0.yml
...@@ -398,7 +398,7 @@ Here are a few examples: ...@@ -398,7 +398,7 @@ Here are a few examples:
* DpnII: ^GATC * DpnII: ^GATC
* BglII: A^GATCT * BglII: A^GATCT
* HindIII: A^AGCTT * HindIII: A^AGCTT
* ARIMA kit: ^GATC,^GANT * ARIMA kit: ^GATC,G^ANTC
Note that multiples restriction motifs can be provided (comma-separated) and Note that multiples restriction motifs can be provided (comma-separated) and
that 'N' base are supported. that 'N' base are supported.
...@@ -419,7 +419,7 @@ Default: 'AAGCTAGCTT' ...@@ -419,7 +419,7 @@ Default: 'AAGCTAGCTT'
--ligation_site '[Ligation motif]' --ligation_site '[Ligation motif]'
``` ```
Exemple of the ARIMA kit: GATCGATC,GATCGANT,GANTGATC,GANTGANT Exemple of the ARIMA kit: GATCGATC,GANTGATC,GANTANTC,GATCANTC
#### `--min_restriction_fragment_size` #### `--min_restriction_fragment_size`
......
# You can use this file to create a conda environment for this pipeline: # You can use this file to create a conda environment for this pipeline:
# conda env create -f environment.yml # conda env create -f environment.yml
name: nf-core-hic-1.2.0dev name: nf-core-hic-1.2.0
channels: channels:
- conda-forge - conda-forge
- bioconda - bioconda
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...@@ -64,7 +64,7 @@ params { ...@@ -64,7 +64,7 @@ params {
// Container slug. Stable releases should specify release tag! // Container slug. Stable releases should specify release tag!
// Developmental code should specify :dev // Developmental code should specify :dev
process.container = 'nfcore/hic:dev' process.container = 'nfcore/hic:1.2.0'
// Load base.config by default for all pipelines // Load base.config by default for all pipelines
includeConfig 'conf/base.config' includeConfig 'conf/base.config'
...@@ -135,7 +135,7 @@ manifest { ...@@ -135,7 +135,7 @@ manifest {
description = 'Analysis of Chromosome Conformation Capture data (Hi-C)' description = 'Analysis of Chromosome Conformation Capture data (Hi-C)'
mainScript = 'main.nf' mainScript = 'main.nf'
nextflowVersion = '>=19.10.0' nextflowVersion = '>=19.10.0'
version = '1.2.0dev' version = '1.2.0'
} }
// Function to ensure that resource requirements don't go beyond // Function to ensure that resource requirements don't go beyond
......
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